Mercurial > repos > peterjc > fasta_filter_by_id
view tools/fasta_tools/fasta_filter_by_id.txt @ 0:2e5f8ad1a096
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:22:24 -0400 |
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children | 5cd569750e85 |
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Galaxy tool to filter FASTA sequences by ID =========================================== This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. See the licence text below. This tool is a short Python script (using the Galaxy library functions) which divides a FASTA file in two, those sequences with or without an ID present in the specified column(s) of a tabular file. Example uses include filtering based on search results from a tool like NCBI BLAST, TMHMM or SignalP. There are just two files to install: * fasta_filter_by_id.py (the Python script) * fasta_filter_by_id.xml (the Galaxy tool definition) The suggested location is next to the similarly names fasta_filter_by_length.py and fasta_filter_by_length.xml files which are included with Galaxy, i.e. in the Galaxy folder tools/fasta_tools You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. The suggested location is next to the fasta_filter_by_length.xml entry. Simply add the line: <tool file="fasta_tools/fasta_filter_by_id.xml" /> That's it. History ======= v0.0.1 - Initial verion (not publicly released) v0.0.2 - Allow both, just pos or just neg output files Developers ========== These wrappers are currently being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: tar -czf fasta_filter_by_id.tar.gz tools/fasta_tools/fasta_filter_by_id.* Check this worked: $ tar -tzf fasta_filter_by_id.tar.gz fasta_tools/fasta_filter_by_id.py fasta_tools/fasta_filter_by_id.txt fasta_tools/fasta_filter_by_id.xml Licence (MIT/BSD style) ======================= Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.